daler / pybedtools

Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
http://daler.github.io/pybedtools
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Support Python 3.10 and 3.11 #383

Closed woutervh closed 1 year ago

woutervh commented 1 year ago

Trying to install pybedtools via conda/mamba in a python 3.11 environment.

It tries to install pybedtools v0.8.2, while 0.9 is released. Is there a specific reason to pin to <3.10? (untested does not imply broken)

> mamba  install --channel conda-forge --channel bioconda pybedtools 

Looking for: ['pybedtools']

conda-forge/linux-64                                        Using cache
conda-forge/noarch                                          Using cache
pkgs/main/linux-64                                            No change
pkgs/r/linux-64                                               No change
pkgs/main/noarch                                              No change
pkgs/r/noarch                                                 No change
bioconda/noarch                                      4.2MB @   4.3MB/s  1.0s
bioconda/linux-64                                    4.5MB @   3.4MB/s  1.4s

Pinned packages:
  - python 3.11.*

Could not solve for environment specs
Encountered problems while solving:
  - package pybedtools-0.8.2-py39h39abbe0_1 requires python >=3.9,<3.10.0a0, but none of the providers can be installed

The environment can't be solved, aborting the operation
daler commented 1 year ago

There's nothing in pybedtools that restricts to Python versions. On the bioconda channel, only up to Python 3.10 is supported -- we're not building for 3.11 yet for any packages.

(see here for py310 pybedtools packages)

Looks like you're trying to install into an environment that already has 3.11 pinned? I actually wouldn't expect any Python packages from bioconda with compiled extensions to be installable in that environment.

If you could provide a requirements.txt or env.yml file that reproduces this in a new env, I could try troubleshooting.